# Hierarchical Methods for Differential Equations

## Documentation for package ‘hmde’ version 1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

hmde-package | The 'hmde' package.
hmde | The 'hmde' package.
hmde_affine_de | Differential equation for affine growth single individual model
hmde_assign_data | Assign data to template for chosen model
hmde_canham_de | Differential equation for Canham growth single and multi- individual models
hmde_const_de | Differential equation for constant growth single and multi- individual models
hmde_extract_estimates | Extract samples and return measurement, individual, and population-level estimates
hmde_extract_Rhat | Calculate Rhat statistics for a hmde_fit object
hmde_model | Select data configuration template for hmde supported model
hmde_model_des | Function to select DE given model name
hmde_model_names | Returns names of available models.
hmde_model_pars | Show parameter list for hmde supported model
hmde_plot_de_pieces | Plot pieces of chosen differential equation model for each individual. Structured to take the individual data tibble that is built by the hmde_extract_estimates function using the ind_par_name_mean estimates. Function piece will go from the first fitted size to the last. Accepted ggplot arguments will change the axis labels, title, line colour, alpha
hmde_plot_obs_est_inds | Plot estimated and observed values over time for a chosen number of individuals based on posterior estimates. Structured to take in the measurement_data tibble constructed by the hmde_extract_estimates function.
hmde_plot_Rhat_hist | Plot histogram of R_hat values for hmde_fit object.
hmde_run | Run chosen pre-built model in Stan
hmde_vb_de | Differential equation for von Bertalanffy growth single and multi- individual models
Lizard_Size_Data | Skink size data - Lampropholis delicata
plot.hmde_model_template | Plot function for hmde_model_template object
print.hmde_model_template | Print function for hmde_model_template object
summary.hmde_model_template | Summary function for hmde_model_template object
Tree_Size_Data | Garcinia recondita - Barro Colorado Island data
Tree_Size_Ests | Garcinia recondita model estimates - Barro Colorado Island data
Trout_Size_Data | SUSTAIN Salmo trutta data